#!/usr/bin/env bash

# 
# 
# 
 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv0.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 20000
perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv0.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 10000
perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv0.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 2000
perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv0.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 200
 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv0.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 20000
perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv0.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 10000
perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv0.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 2000
perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv0.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 0


perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv1.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 20000
perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv1.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 10000
perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv1.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 2000
perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv1.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 200
 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv1.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 20000
 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv1.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 10000
 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv1.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 2000
 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv1.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 0


 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv3.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 20000
perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv3.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 10000
 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv3.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 2000
 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv3.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 200
 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv3.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 20000
 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv3.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 10000
 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv3.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 2000
 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv3.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 0

perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv4.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 20000
perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv4.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 10000
perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv4.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 2000
perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/normal.cnv4.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_normalMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 200
perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv4.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 20000
 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv4.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 10000
 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv4.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 2000
 perl   overlap_CNV.pl /Users/yaping/Documents/lab/project/CNV-SNP-Methylation/tumor.cnv4.bed /Users/yaping/Documents/workspace/result/ASM/methylCGsRich_ASM_AllSnp_tumorMerge_sigASMGroup-5-1-0.01-unjustedP.gtf 0




